Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

The landscape of RNA polymerase II-associated chromatin interactions in prostate cancer

ABSTRACT: The landscape of RNA polymerase II-associated chromatin interactions in prostate cancer

PROVIDER: PRJNA495368 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR7988010.fastq.gz	Fastqsanger.gz
	SRR7988020.fastq.gz	Fastqsanger.gz
	SRR7988012.fastq.gz	Fastqsanger.gz
	SRR7988022.fastq.gz	Fastqsanger.gz
	SRR7988014.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 10

Similar Datasets

The landscape of RNA polymerase II-associated chromatin interactions in prostate cancer

Project description:The landscape of RNA polymerase II-associated chromatin interactions in prostate cancer

| PRJNA495365 | ENA

The landscape of RNA polymerase II-associated chromatin interactions in prostate cancer

Project description:The landscape of RNA polymerase II-associated chromatin interactions in prostate cancer

| PRJNA495369 | ENA

The landscape of RNA polymerase II-associated chromatin interactions in prostate cancer

Project description:Three dimensional genome maps of the transcriptional machinery in prostate cancer cells.

2020-04-27 | GSE121020 | GEO

The landscape of RNA polymerase II-associated chromatin interactions in prostate cancer.

Project description:Transcriptional dysregulation is a hallmark of prostate cancer (PCa). We mapped the RNA polymerase II-associated (RNA Pol II-associated) chromatin interactions in normal prostate cells and PCa cells. We discovered thousands of enhancer-promoter, enhancer-enhancer, as well as promoter-promoter chromatin interactions. These transcriptional hubs operate within the framework set by structural proteins - CTCF and cohesins - and are regulated by the cooperative action of master transcription factors, such as the androgen receptor (AR) and FOXA1. By combining analyses from metastatic castration-resistant PCa (mCRPC) specimens, we show that AR locus amplification contributes to the transcriptional upregulation of the AR gene by increasing the total number of chromatin interaction modules comprising the AR gene and its distal enhancer. We deconvoluted the transcription control modules of several PCa genes, notably the biomarker KLK3, lineage-restricted genes (KRT8, KRT18, HOXB13, FOXA1, ZBTB16), the drug target EZH2, and the oncogene MYC. By integrating clinical PCa data, we defined a germline-somatic interplay between the PCa risk allele rs684232 and the somatically acquired TMPRSS2-ERG gene fusion in the transcriptional regulation of multiple target genes - VPS53, FAM57A, and GEMIN4. Our studies implicate changes in genome organization as a critical determinant of aberrant transcriptional regulation in PCa.

| S-EPMC7410051 | biostudies-literature

The landscape of RNA polymerase II-associated chromatin interactions in prostate cancer

Project description:The goal of the study is to profile the gene expression signatures in prosate cancer models.

2020-04-27 | GSE121022 | GEO

The landscape of RNA polymerase II-associated chromatin interactions in prostate cancer

Project description:Genome wide occupany of CTCF, H3K27ac and AR

2020-04-27 | GSE121021 | GEO

RNA polymerase II is necessary for enhancer-promoter interactions.

Project description:Enhancer-promoter interactions and their interplay between CTCF-cohesin are assumed that regulate gene expression. Here, we use Micro-C sequencing instead of Hi-C sequencing to explore whole-genome E-P interactions in an auxin-mediated degradation of RNA polymerase II cell line.

2022-07-05 | GSE178593 | GEO

RNA polymerase II is necessary for enhancer-promoter interactions.

Project description:RNA polymerase II is necessary for enhancer-promoter interactions.

| PRJNA739703 | ENA

The landscape of RNA polymerase II transcription initiation in C. elegans reveals a novel regulatory architecture

Project description:It has recently been shown that RNA Polymerase II transcription is far more extensive than previously thought, much of it not associated with protein-coding genes. To investigate this phenomenon, we determined the genome-wide landscape of RNA Polymerase II transcription initiation and elongation in C. elegans. We identify 73,500 distinct clusters of transcription initiation and find that initiation is often bidirectional. Strikingly, the majority of initiation events occur in regions with enhancer-like chromatin signatures. We also assign transcription initiation sites to 7691 protein coding genes, the majority previously unknown because of trans-splicing. Through mapping RNA PolII initiation (short capped RNAs) and elongation (long capped RNAs), we provide identification of transcription start sites.

2013-03-29 | E-GEOD-42819 | biostudies-arrayexpress

Maintenance of Long-Range DNA Interactions after Inhibition of Ongoing RNA Polymerase II Transcription.

Project description:A relationship exists between nuclear architecture and gene activity and it has been proposed that the activity of ongoing RNA polymerase II transcription determines genome organization in the mammalian cell nucleus. Recently developed 3C and 4C technology allowed us to test the importance of transcription for nuclear architecture. We demonstrate that upon transcription inhibition binding of RNA polymerase II to gene regulatory elements is severely reduced. However, contacts between regulatory DNA elements and genes in the Î²-globin locus are unaffected and the locus still interacts with the same genomic regions elsewhere on the chromosome. This is a general phenomenon since the great majority of intra- and interchromosomal interactions with the ubiquitously expressed Rad23a gene are also not affected. Our data demonstrate that without transcription the organization and modification of nucleosomes at active loci and the local binding of specific trans-acting factors is unaltered. We propose that these parameters, more than transcription or RNA polymerase II binding, determine the maintenance of long-range DNA interactions. Keywords: transcription inhibition 4C 4C experiments were performed in duplo, dye swap was included. Hybridisation was performed on dedicated micro-arrays. Probes (60-mers) were selected from the sequences 100 bp up âand downstream of HindIII sites. To prevent cross-hybridization, probes that had any similarity with highly abundant repeats (RepBase 10.09) were removed from the probeset. In addition, probes that gave more than two BLAST hits in the genome were also removed from the probeset. Sequence alignments were performed using MegaBLAST using the standard settings. A hit was defined as an alignment of 30 nt or longer.

2010-05-26 | E-GEOD-10170 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data